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Overview of Key ICM Features

Overview of Key ICM Features. NIBR - Emeryville July 10-11 2012. Introduction to MolSoft. Established in 1994 Privately owned Worldwide customer base in academia, pharma and biotech Many published success stories in comp bio & chem. Support. E-mail andy@molsoft.com

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Overview of Key ICM Features

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  1. Overview of Key ICM Features NIBR - Emeryville July 10-11 2012

  2. Introduction to MolSoft • Established in 1994 • Privately owned • Worldwide customer base in academia, pharma and biotech • Many published success stories in comp bio & chem

  3. Support E-mail andy@molsoft.com support@molsoft.com Call: 858-625-2000 x108 www.molsoft.com/news.html

  4. Molecule Visualization • Store in a single file: • Representations • Lighting/Depth • Multiple Slides • Multiple Viewpoints • Annotation • Rendering • Parametric Animations • Alignments • Chemical Tables Product: ICM-Browser & ActiveICM

  5. iMolview for the iPad and iPhone

  6. Bioinformatics • Fully interactive alignments • Trees • Sequence and alignments directly linked to 3D structure • Rich alignment editor • Sequence search PDB, Uniprot etc…

  7. Structure Analysis • Calculate • RMSD • Contact Areas • Surface Areas • Measure distances and angles (planar, dihedral) • Fully interactive Ramachandran Plots • Protein Superposition

  8. Structure Prediction • Identify closed cavities • Identify ligand binding sites (An et al 2005 & Kufareva et al 2012) • Identify protein-protein interaction sites (Fernandez-Recio et al 2005) • Protein health An, J., Totrov, M., and Abagyan, R. (2005). Pocketome Via Comprehensive Identification and Classification of Ligand Binding Envelopes. Mol Cell Proteomics 4, 752–761. • Kufareva I, Ilatovskiy AV, Abagyan R. Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 2012 Jan;40(Database issue):D535-40. • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins. 2005 Jan 1;58(1):134-43

  9. Crystallographic Analysis • Neighbors • Cell • Biomolecule generator • Display and contour electron density maps

  10. Homology Modeling • Build homology models (Katritch et al 2010) • Refine models • Predict and/or design loop conformation • Search loop databases • New loop modeling force-field (Arnautova et al 2011) Arnautova YA, Abagyan RA, Totrov M. Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins. 2011 Feb;79(2):477-98. • Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R. GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins. 2010 Jan;78(1):197-211

  11. 3D Interactive Ligand Editor • Interactively edit a ligand bound to a receptor in 3D. • Screen for best replacement group • Join fragments by linkers. • Edit ligand in 2D molecular editor. • Delete atoms and bonds. • Convenient undo and redo modification feature. • Dock and/or minimize edited ligand. • Fragment docking. • Multiple receptor docking • Restrain atoms during docking

  12. Cheminformatics • 2D ligand sketcher • Fully interactive chemical spreadsheets and plots • Chemical clustering • Chemical searching • Library enumeration • Pharmacophore searching

  13. Atomic Property Fields A continuous, multi-component 3D potential that reflects preferences for various atomic properties at each point in space. Totrov M. Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites. BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S35. Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. Spatial chemical distance based on atomic property fields. J Comput Aided Mol Des. 2010 Mar;24(3):173-82. Totrov M. Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. ChemBiol Drug Des. 2008 Jan;71(1):15-27.

  14. Docking & Screening • Small molecule docking • Protein-protein docking • Template docking • Induced Fit Docking • Multiple Receptors • Explicit Groups • Tethered Docking • Virtual Screening • Structure-based • Ligand- based APF See: www.molsoft.com/vls for success stories

  15. ICMDB • What is it? • A single, unified client for data entry, mining and manipulation built into a powerful chemistry and bio-enabled platform • Prerequisites • One or multiple (possibly existing) relational databases with research data related to biology and chemistry • Deployment • A cross-platform client • Installs transparently on top of existing databases

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